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Fusion Protein:CDC5L-VEGFA |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: CDC5L-VEGFA | FusionPDB ID: 14927 | FusionGDB2.0 ID: 14927 | Hgene | Tgene | Gene symbol | CDC5L | VEGFA | Gene ID | 988 | 7422 |
| Gene name | cell division cycle 5 like | vascular endothelial growth factor A | |
| Synonyms | CDC5|CDC5-LIKE|CEF1|PCDC5RP|dJ319D22.1 | MVCD1|VEGF|VPF | |
| Cytomap | 6p21.1 | 6p21.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cell division cycle 5-like proteinCDC5 cell division cycle 5-likeCdc5-related proteindJ319D22.1 (CDC5-like protein)pombe cdc5-related protein | vascular endothelial growth factor Avascular endothelial growth factor A121vascular endothelial growth factor A165vascular permeability factor | |
| Modification date | 20200313 | 20200329 | |
| UniProtAcc | Q99459 Main function of 5'-partner protein: FUNCTION: DNA-binding protein involved in cell cycle control. May act as a transcription activator. Plays role in pre-mRNA splicing as core component of precatalytic, catalytic and postcatalytic spliceosomal complexes (PubMed:11991638, PubMed:20176811, PubMed:28502770, PubMed:28076346, PubMed:29361316, PubMed:29360106, PubMed:29301961, PubMed:30728453, PubMed:30705154). Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. The PRP19-CDC5L complex may also play a role in the response to DNA damage (DDR) (PubMed:20176811). {ECO:0000269|PubMed:10570151, ECO:0000269|PubMed:11082045, ECO:0000269|PubMed:11101529, ECO:0000269|PubMed:11544257, ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:12927788, ECO:0000269|PubMed:18583928, ECO:0000269|PubMed:20176811, ECO:0000269|PubMed:24332808, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:29301961, ECO:0000269|PubMed:29360106, ECO:0000269|PubMed:29361316, ECO:0000269|PubMed:30705154, ECO:0000269|PubMed:30728453, ECO:0000269|PubMed:9038199, ECO:0000269|PubMed:9468527, ECO:0000269|PubMed:9632794}. | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000371477, | ENST00000230480, ENST00000372064, ENST00000372077, ENST00000425836, ENST00000457104, ENST00000482630, ENST00000518689, ENST00000518824, ENST00000520948, ENST00000523125, ENST00000523873, ENST00000523950, ENST00000372055, ENST00000372067, ENST00000417285, ENST00000324450, ENST00000413642, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 10 X 4 X 7=280 | 10 X 9 X 5=450 |
| # samples | 11 | 13 | |
| ** MAII score | log2(11/280*10)=-1.34792330342031 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(13/450*10)=-1.79141337818858 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Fusion gene context | PubMed: CDC5L [Title/Abstract] AND VEGFA [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: CDC5L [Title/Abstract] AND VEGFA [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CDC5L(44376369)-VEGFA(43752278), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | CDC5L-VEGFA seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CDC5L-VEGFA seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CDC5L-VEGFA seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. CDC5L-VEGFA seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. CDC5L-VEGFA seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. CDC5L-VEGFA seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. CDC5L-VEGFA seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF. | ||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | CDC5L | GO:0000398 | mRNA splicing, via spliceosome | 28076346 |
| Hgene | CDC5L | GO:0045944 | positive regulation of transcription by RNA polymerase II | 11082045 |
| Tgene | VEGFA | GO:0000122 | negative regulation of transcription by RNA polymerase II | 18093989 |
| Tgene | VEGFA | GO:0001525 | angiogenesis | 11427521|21771332 |
| Tgene | VEGFA | GO:0001666 | response to hypoxia | 16490744 |
| Tgene | VEGFA | GO:0001934 | positive regulation of protein phosphorylation | 18386220|19033661 |
| Tgene | VEGFA | GO:0001938 | positive regulation of endothelial cell proliferation | 9202027|10022831|12714610|16489009|18386220|18577655|20497126 |
| Tgene | VEGFA | GO:0002042 | cell migration involved in sprouting angiogenesis | 18059339|20660291 |
| Tgene | VEGFA | GO:0002092 | positive regulation of receptor internalization | 20660291 |
| Tgene | VEGFA | GO:0008284 | positive regulation of cell proliferation | 7929439 |
| Tgene | VEGFA | GO:0008360 | regulation of cell shape | 7929439|10527820 |
| Tgene | VEGFA | GO:0010595 | positive regulation of endothelial cell migration | 10022831|19033661 |
| Tgene | VEGFA | GO:0010628 | positive regulation of gene expression | 18386220 |
| Tgene | VEGFA | GO:0010629 | negative regulation of gene expression | 28977001 |
| Tgene | VEGFA | GO:0010749 | regulation of nitric oxide mediated signal transduction | 16150726 |
| Tgene | VEGFA | GO:0030224 | monocyte differentiation | 21149635 |
| Tgene | VEGFA | GO:0030225 | macrophage differentiation | 21149635 |
| Tgene | VEGFA | GO:0030335 | positive regulation of cell migration | 7929439|17470632 |
| Tgene | VEGFA | GO:0030949 | positive regulation of vascular endothelial growth factor receptor signaling pathway | 1312256|7929439 |
| Tgene | VEGFA | GO:0031334 | positive regulation of protein complex assembly | 16489009|19033661 |
| Tgene | VEGFA | GO:0031954 | positive regulation of protein autophosphorylation | 20497126 |
| Tgene | VEGFA | GO:0032147 | activation of protein kinase activity | 18059339|20497126 |
| Tgene | VEGFA | GO:0032793 | positive regulation of CREB transcription factor activity | 20497126 |
| Tgene | VEGFA | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 18440775|20497126 |
| Tgene | VEGFA | GO:0035148 | tube formation | 19033661 |
| Tgene | VEGFA | GO:0035767 | endothelial cell chemotaxis | 18440775 |
| Tgene | VEGFA | GO:0035924 | cellular response to vascular endothelial growth factor stimulus | 18440775|20497126 |
| Tgene | VEGFA | GO:0038033 | positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway | 18440775|20497126|21245381 |
| Tgene | VEGFA | GO:0038091 | positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | 17470632 |
| Tgene | VEGFA | GO:0042531 | positive regulation of tyrosine phosphorylation of STAT protein | 19390056 |
| Tgene | VEGFA | GO:0043117 | positive regulation of vascular permeability | 26598555 |
| Tgene | VEGFA | GO:0043154 | negative regulation of cysteine-type endopeptidase activity involved in apoptotic process | 18386220 |
| Tgene | VEGFA | GO:0043406 | positive regulation of MAP kinase activity | 18440775 |
| Tgene | VEGFA | GO:0043536 | positive regulation of blood vessel endothelial cell migration | 9202027|18440775|20497126 |
| Tgene | VEGFA | GO:0045766 | positive regulation of angiogenesis | 18440775|18577655|19033661|20497126 |
| Tgene | VEGFA | GO:0045785 | positive regulation of cell adhesion | 19674970 |
| Tgene | VEGFA | GO:0045944 | positive regulation of transcription by RNA polymerase II | 18059339 |
| Tgene | VEGFA | GO:0048010 | vascular endothelial growth factor receptor signaling pathway | 21245381 |
| Tgene | VEGFA | GO:0050731 | positive regulation of peptidyl-tyrosine phosphorylation | 10022831|16489009|20048167|21245381|26598555 |
| Tgene | VEGFA | GO:0050918 | positive chemotaxis | 20497126 |
| Tgene | VEGFA | GO:0050927 | positive regulation of positive chemotaxis | 7929439|12744932 |
| Tgene | VEGFA | GO:0051272 | positive regulation of cellular component movement | 10527820|12744932 |
| Tgene | VEGFA | GO:0051894 | positive regulation of focal adhesion assembly | 16489009 |
| Tgene | VEGFA | GO:0071456 | cellular response to hypoxia | 10575000 |
| Tgene | VEGFA | GO:0090037 | positive regulation of protein kinase C signaling | 18059339 |
| Tgene | VEGFA | GO:0090050 | positive regulation of cell migration involved in sprouting angiogenesis | 20551324 |
| Tgene | VEGFA | GO:0097533 | cellular stress response to acid chemical | 26299712 |
| Tgene | VEGFA | GO:1900086 | positive regulation of peptidyl-tyrosine autophosphorylation | 20660291 |
| Tgene | VEGFA | GO:1900745 | positive regulation of p38MAPK cascade | 18386220 |
| Tgene | VEGFA | GO:1901727 | positive regulation of histone deacetylase activity | 20497126 |
| Tgene | VEGFA | GO:1903141 | negative regulation of establishment of endothelial barrier | 20048167 |
| Tgene | VEGFA | GO:1903392 | negative regulation of adherens junction organization | 26598555 |
| Tgene | VEGFA | GO:1903572 | positive regulation of protein kinase D signaling | 20497126 |
| Tgene | VEGFA | GO:1903672 | positive regulation of sprouting angiogenesis | 26299712 |
| Tgene | VEGFA | GO:2000048 | negative regulation of cell-cell adhesion mediated by cadherin | 26598555 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:44376369/chr6:43752278) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Retention analysis results of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features, are available here. |
| Fusion gene breakpoints across CDC5L (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across VEGFA (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Amino Acid Sequences |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000371477 | CDC5L | chr6 | 44376369 | + | ENST00000324450 | VEGFA | chr6 | 43752278 | + | 1413 | 1391 | 275 | 1396 | 373 |
| ENST00000371477 | CDC5L | chr6 | 44376369 | + | ENST00000413642 | VEGFA | chr6 | 43752278 | + | 1440 | 1391 | 275 | 1396 | 373 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000371477 | ENST00000324450 | CDC5L | chr6 | 44376369 | + | VEGFA | chr6 | 43752278 | + | 0.001572438 | 0.9984276 |
| ENST00000371477 | ENST00000413642 | CDC5L | chr6 | 44376369 | + | VEGFA | chr6 | 43752278 | + | 0.001594428 | 0.99840564 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
Get the fusion protein sequences from here. |
| Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for CDC5L-VEGFA |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
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Potential FusionNeoAntigen Information of CDC5L-VEGFA in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Potential FusionNeoAntigen Information of CDC5L-VEGFA in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * We used NetMHCIIpan v4.1 (%rank<0.5). |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of CDC5L-VEGFA |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDC5L-VEGFA |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
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Vaccine Design for the FusionNeoAntigens of CDC5L-VEGFA |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of CDC5L-VEGFA |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
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Potential target of CAR-T therapy development for CDC5L-VEGFA |
| Predicted 3D structure. We used RoseTTAFold. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * Minus value of BPloci means that the break point is located before the CDS. |
| - In-frame and retained 'Transmembrane'. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
| Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to CDC5L-VEGFA |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CDC5L-VEGFA |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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